PROGRAM: indelFit
USAGE: indelFit [OPTIONS] indel-history.ih tree.nh > out
DESCRIPTION:
Estimate the parameters of a simple indel model, given an indel history
and a tree. By default, writes estimates of three parameters to
stdout: an insertion rate alpha, a deletion rate beta, and a parameter
tau roughly equal to the inverse of the expected indel length (modulo
adjustments required to make probabilities sum to one).
An indel history can be obtained with indelHistory and a tree with
phyloFit.
OPTIONS:
--alpha, -a
Starting value of alpha, the insertion rate. Default is 0.02.
--beta, -b
Starting value of beta, the deletion rate. Default is 0.04.
--tau, -t
Starting value of tau, the length parameter. Default is 0.05.
--lnl, -L
Compute log likelihood of model only, without optimizing parameters.
The options above can be used to set the parameters as desired.
--columns, -c
Output log likelihood of each column.
--features, -f
Estimate separate parameters for each type of feature in the given
file, as well as for background sites.
--reference, -r
(For use with --features) Name of species (node of tree) defining
coordinate frame of features. By default, the coordinate frame of
the entire alignment is assumed.
--log, -l
Write log of optimization to specified file.
--help, -h
Display this help message and exit.